3DR2

Structural and Functional Analyses of XC5397 from Xanthomonas campestris: A Gluconolactonase Important in Glucose Secondary Metabolic Pathways


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The First Crystal Structure of Gluconolactonase Important in the Glucose Secondary Metabolic Pathways

Chen, C.-N.Chin, K.-H.Wang, A.H.-J.Chou, S.-H.

(2008) J.Mol.Biol. 384: 604-614

  • DOI: 10.1016/j.jmb.2008.09.055

  • PubMed Abstract: 
  • The first gluconolactonase crystal structure from bacteria has been determined to a resolution of 1.61 A using X-ray crystallography. It belongs to the senescence marker protein 30/gluconolaconase superfamily but exhibits substrate specificity mainly ...

    The first gluconolactonase crystal structure from bacteria has been determined to a resolution of 1.61 A using X-ray crystallography. It belongs to the senescence marker protein 30/gluconolaconase superfamily but exhibits substrate specificity mainly toward D-glucono-delta-lactone. It forms a novel disulfide-bonded clamshell dimer comprising two doughnut-shaped six-bladed beta-propeller domains, yet with an exceptionally long N-terminal subdomain forming an extra helix and four additional beta-strands to enclose half of the outermost beta-strands of each propeller. Extensive interactions, including H-bonds, salt bridges, disulfide bonds, and coordination bonds, along with numerous bridging water molecules, are present in the interface to institute the "top-to-top" clamshell-type dimer. Three calcium ions per subunit were observed. Two are present in the central water-filled channel, with the top one coordinated to four highly conserved amino acids and is possibly involved in substrate hydrolysis, while the bottom one is coordinated to the backbone oxygen atoms, which is possibly for stabilizing the propeller domain. One calcium ion is situated in the interface also to stabilize the dimer form. Since gluconolactonase is essential in the glucose secondary metabolic pathways leading to the synthesis of pentose, vitamin C, or "antiaging" factors, determination of its tertiary structure should help understand these important biochemical processes.


    Organizational Affiliation

    Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exported gluconolactonase
A, B
305Xanthomonas campestris pv. campestris (strain B100)Gene Names: gnl1
EC: 3.1.1.17
Find proteins for B0RN69 (Xanthomonas campestris pv. campestris (strain B100))
Go to UniProtKB:  B0RN69
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.541α = 90.00
b = 89.741β = 127.71
c = 85.228γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
SOLVEphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance